URMC / Biochemistry & Biophysics / Research / Recent Publications Recent Publications Mittal ATurner DHMathews DH NNDB: An expanded database of nearest neighbor parameters for predicting stability of nucleic acid secondary structures.; Journal of molecular biology. 2024 Mar 22. Beard JWHunt SLEvans AGoenner CMiller BL Mimicking an in cellulo environment for enzyme-free paper-based nucleic acid tests at the point of care.; bioRxiv : the preprint server for biology. 2024 Feb 29. Sherina VMcMurray HRPowers WLand HLove TMTMcCall MN Correction: Multiple imputation and direct estimation for qPCR data with non-detects.; BMC bioinformatics; Vol 25(1), pp. 63. 2024 Feb 07. Hoare MTan RWelle KASwovick KHryhorenko JRGhaemmaghami S Methionine Alkylation as an Approach to Quantify Methionine Oxidation Using Mass Spectrometry.; Journal of the American Society for Mass Spectrometry. 2024 Feb 07. Jonnakuti VSWagner EJMaletić-Savatić MLiu ZYalamanchili HK PolyAMiner-Bulk is a deep learning-based algorithm that decodes alternative polyadenylation dynamics from bulk RNA-seq data.; Cell reports methods. 2024 Feb 03. Alessandrini FWright MKurosaki TMaquat LEKiskinis E ALS-Associated TDP-43 Dysfunction Compromises UPF1-Dependent mRNA Metabolism Pathways Including Alternative Polyadenylation and 3'UTR Length.; bioRxiv : the preprint server for biology. 2024 Feb 02. Tan RHoare MBellomio PBroas SCamacho KSwovick KWelle KHryhorenko JGhaemmaghami S Formylation facilitates the reduction of oxidized initiator methionines; bioRxiv. 2024 Jan 01. De Zoysa THauke ACIyer NRMarcus EOstrowski SMStegemann FErmolenko DNFay JCPhizicky EM A connection between the ribosome and two S. pombe tRNA modification mutants subject to rapid tRNA decay.; PLoS genetics; Vol 20(1), pp. e1011146. 2024 Jan 31. Kurosaki TRambout XMaquat LE FMRP-mediated spatial regulation of physiologic NMD targets in neuronal cells.; Genome biology; Vol 25(1), pp. 31. 2024 Jan 23. Tumenbayar BITutino VMBrazzo JAYao PBae Y FAK and p130Cas modulate stiffness-mediated early transcription and cellular metabolism.; bioRxiv : the preprint server for biology. 2024 Jan 16. Chen JLLeeder WMMorais PAdachi HYu YT Pseudouridylation-mediated gene expression modulation.; The Biochemical journal; Vol 481(1), pp. 1-16. 2024 Jan 10. Rasmussen ALGronvall GKLowen ACGoodrum FAlwine JAndersen KGAnthony SJBaines JBanerjee ABroadbent AJBrooke CBCampos SKCaposio PCasadevall AChan GCCliffe ARCollins-McMillen DConnell NDamania BDaugherty MDDebbink KDermody TSDiMaio DDuprex WPEmerman MGalloway DAGarry RFGoldstein SAGreninger ALHartman ALHogue BGHorner SMHotez PJJung JUKamil JPKarst SMLaimins LLakdawala SSLandais ILetko MLindenbach BLiu S-LLuftig MMcFadden GMehle AMorrison JMoscona AMühlberger EMunger JMünger KMurphy ENeufeldt CJNikolich JZO'Connor CMPekosz APermar SRPfeiffer JKPopescu SVPurdy JGRacaniello VRRice CMRunstadler JASapp MJScott RSSmith GASorrell EMSperanza EStreblow DTibbetts SAToth ZVan Doorslaer KWeiss SRWhite EAWhite TMWobus CEWorobey MYamaoka SYurochko A Virology-the path forward.; Journal of virology. 2024 Jan 03. Wu JHollinger JBonanno EJiang FYao P Cardiomyocyte-Specific Loss of Glutamyl-prolyl-tRNA Synthetase Leads to Disturbed Protein Homeostasis and Dilated Cardiomyopathy.; Cells; Vol 13(1). 2023 Dec 22. Hasper JWelle KSwovick KHryhorenko JGhaemmaghami SBuchwalter A Long lifetime and tissue-specific accumulation of lamin A/C in Hutchinson-Gilford progeria syndrome.; The Journal of cell biology; Vol 223(1). 2023 Nov 15. Meadow MBroas SHoare MAlimohammadi FWelle KSwovick KHryhorenko JMartinez JBiashad SSeluanov AGorbunova VBuchwalter AGhaemmaghami S Proteome birthdating reveals age-selectivity of protein ubiquitination; bioRxiv. 2023 Jan 01. Poruthoor AJSharma AGrossfield A Understanding the Free Energy Landscape of Phase Separation in Lipid Bilayers using Molecular Dynamics.; Biophysical journal. 2023 Sep 22. Wu JHollinger JBonanno EJiang FYao P Cardiomyocyte-specific Loss of Glutamyl-prolyl-tRNA Synthetase Leads to Disturbed Protein Homeostasis and Dilated Cardiomyopathy.; bioRxiv : the preprint server for biology. 2023 Sep 22. De Zoysa THauke ACIyer NRMarcus EOstrowski SMFay JCPhizicky EM A connection between the ribosome and two S. pombe tRNA modification mutants subject to rapid tRNA decay.; bioRxiv : the preprint server for biology. 2023 Sep 18. Pham TMMiffin TSun HSharp KKWang XZhu MHoshika SPeterson RJBenner SAKahn JDMathews DH DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.; ACS synthetic biology. 2023 Sep 06. Boutz PL Putting a finger on histidine methylation.; Genes & development; Vol 37(15-16), pp. 675-677. 2023 Sep 06.